Shower caulk bubbling up -

I have a marble tile shower that I saw being built about 6 years ago. After reading other postings in the forum, it seems that it was built correctly. Sloped floor, membrane up and over the sill and up the wall, CBU, and moisture barrier. The horizontal corners and the vertical corners were caulked and the rest was grouted. However, recently the caulk in the floor/wall joint has bubbled up near the front of the shower.

I removed the caulk, fixed a couple of small cracks in the grout, regrouted, recaulked, and resealed. The caulk bubbled up again (in the same places) after about 3 months despite wiping the shower dry after each use. When removing the caulk around the perimeter of the shower floor I noticed it was wet and very soft near the front of the shower; the caulk in the back of the shower was dry and very solid.

I have checked for external leaks and find no evidence of water getting behind the escutcheon, no plumbing pipe/joint leaks, and no water or evidence of water in the basement where I can see the base of the shower. It appears that the shower pan is doing its job, but I'm looking for suggestions on where is the water coming from? How do I fix this joint? What steps should I take to find and resolve this problem? Thank you.

It's difficult to picture what you mean by caulk "bubbling up". A photo would help immensely here.
What kind of caulk? An appropriate caulk for a shower does not get "soft" when exposed to water, nor
does it get "hard" when dry. The application area must be perfectly (perfectly!) dry before caulk application.
The moisture is likely migrating from hairline cracks in the grout/marble above. There is no such thing as a
"permanent" caulk job - it's a maintenance item. Its main function is decorative, and to keep crud from
accumulating in the corners.

Was the liner installed flat on the floor or was it installed over a pre-sloped mortar bed? If it is in the wrong place (flat on the floor), it won't leak, but it will retain moisture, making the whole shower become saturated. this has nothing to do with the fact the top layer is sloped...the waterproofing layer (the liner) must be sloped as well. About 6-years is the right timing for the mortar to become saturated if either the liner is flat on the floor or the weepholes are plugged. Some stones will hold a fair amount of moisture if in contact with saturated mudbeds, and this can make caulk problematic.

Thank you for the quick responses. No pictures are available, I've already removed the caulk. The old caulk was color matching sanded siliconized acrylic caulk by Color Caulk, Inc. Aurora IL. Bubbling meant that the caulk had softened and expanded due to constant contact with water. The hard caulk wasn't hard per se, but it was solid and solidly attached to the tiles. I know the membrane was placed on the slant and not on the floor (I have wood floors over open trusses) When I dug out the caulk in the perimeter this time (and the first time), it was wet beneath the caulk.

Is there a way to inspect/clean the weep holes?

I have removed all of the perimeter caulk and I will let it sit for a few weeks before I use some denatured alcohol to dry/clean the joint and then re-caulk. The joint is 1/4 to 1/2 inch deep.... should I use backer bar or just use multiple layers of caulk to build it up? Thanks for your help.

Backer rod makes for a superior caulk joint. It forces the caulk into an hour-glass shape so it can stretch easier. A solid block may be strong enough to pull itself off the side when it tries to stretch.